Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
Collapse
 
  • Page of 1
  • Filter
  • Time
  • Show
Clear All
new posts
Previous template Next
  • #1

    IMonitor and Immunoglobulin Galaxy

    Has any of you installed/used one of these software?

    IMonitor
    Immunoglobulin Galaxy
    Tags: None
  • #2
    ImmunoGlobulin galaxy (IGGalaxy) for simple determination and quantitation of immunoglobulin heavy chain rearrangements from NGS - BMC Immunology
    http://bmcimmunol.biomedcentral.com/articles/10.1186/s12865-014-0059-7
    Background Sequence analysis of immunoglobulin heavy chain (IGH) gene rearrangements and frequency analysis is a powerful tool for studying the immune repertoire, immune responses and immune dysregulation in health and disease. The challenge is to provide user friendly, secure and reproducible analytical services that are available for both small and large laboratories which are determining VDJ repertoire using NGS technology. Results In this study we describe ImmunoGlobulin Galaxy (IGGalaxy)- a convenient web based application for analyzing next-generation sequencing results and reporting IGH gene rearrangements for both repertoire and clonality studies. IGGalaxy has two analysis options one using the built in igBLAST algorithm and the second using output from IMGT; in either case repertoire summaries for the B-cell populations tested are available. IGGalaxy supports multi-sample and multi-replicate input analysis for both igBLAST and IMGT/HIGHV-QUEST. We demonstrate the technical validity of this platform using a standard dataset, S22, used for benchmarking the performance of antibody alignment utilities with a 99.9 % concordance with previous results. Re-analysis of NGS data from our samples of RAG-deficient patients demonstrated the validity and user friendliness of this tool. Conclusions IGGalaxy provides clinical researchers with detailed insight into the repertoire of the B-cell population per individual sequenced and between control and pathogenic genomes. IGGalaxy was developed for 454 NGS results but is capable of analyzing alternative NGS data (e.g. Illumina, Ion Torrent). We demonstrate the use of a Galaxy virtual machine to determine the VDJ repertoire for reference data and from B-cells taken from immune deficient patients. IGGalaxy is available as a VM for download and use on a desktop PC or on a server.


    http://www.genetics.org/content/early/2015/08/21/genetics.115.176735

    Comment

    Previous template Next

    Latest Articles

    Collapse
    • seqadmin
      Essential Discoveries and Tools in Epitranscriptomics
      by seqadmin




      The field of epigenetics has traditionally concentrated more on DNA and how changes like methylation and phosphorylation of histones impact gene expression and regulation. However, our increased understanding of RNA modifications and their importance in cellular processes has led to a rise in epitranscriptomics research. “Epitranscriptomics brings together the concepts of epigenetics and gene expression,” explained Adrien Leger, PhD, Principal Research Scientist...
      04-22-2024, 07:01 AM
    • seqadmin
      Current Approaches to Protein Sequencing
      by seqadmin


      Proteins are often described as the workhorses of the cell, and identifying their sequences is key to understanding their role in biological processes and disease. Currently, the most common technique used to determine protein sequences is mass spectrometry. While still a valuable tool, mass spectrometry faces several limitations and requires a highly experienced scientist familiar with the equipment to operate it. Additionally, other proteomic methods, like affinity assays, are constrained...
      04-04-2024, 04:25 PM
    View All

    ad_right_rmr

    Collapse

    News

    Collapse
    Topics Statistics Last Post
    Expanding the Horizons of Cellular Research with the Single Cell Atlas by seqadmin
    Started by seqadmin, Yesterday, 11:49 AM
    0 responses
    15 views
    0 likes
    		 Last Post seqadmin
    by seqadmin
    Yesterday, 11:49 AM  
    Genetic Variants and Diabetes Risk in Childhood Cancer Survivors by seqadmin
    Started by seqadmin, 04-24-2024, 08:47 AM
    0 responses
    16 views
    0 likes
    		 Last Post seqadmin
    by seqadmin
    04-24-2024, 08:47 AM  
    Cancer Metastasis: A Deep Dive into Cellular Plasticity by seqadmin
    Started by seqadmin, 04-11-2024, 12:08 PM
    0 responses
    61 views
    0 likes
    		 Last Post seqadmin
    by seqadmin
    04-11-2024, 12:08 PM  
    Proteogenomic Profiles Offer New Clues in Prostate Cancer by seqadmin
    Started by seqadmin, 04-10-2024, 10:19 PM
    0 responses
    60 views
    0 likes
    		 Last Post seqadmin
    by seqadmin
    04-10-2024, 10:19 PM  
    View All
    Working...
    X